Biology subjects

Wagner, B. D.

Publications and source records attributed to Wagner, B. D..

4 recordsLinked to original sources

bioRxiv2025

Integrative Multi-Omics Analysis of Melanoma: Uncovering Pathways Associated with Immunotherapy Outcomes

PurposeThe treatment of advanced malignant melanoma with immune checkpoint blockade (ICB) therapies such as anti-CTLA4 and anti-PD1 has been transformative, yet a significant proportion of patients demonstrate intrinsic resistance or develop severe immune-related adverse events (irAEs), complicating treatment strategies. This study aimed to integrate clinical and molecular data using multi-omics factor analysis (MOFA) To better understand the multifaceted interactions governing ICB resistance and irAE development. MethodsMelanoma patient-derived xenograft tumors with transcriptomic and microbiome data were analyzed using the MOFA2 R package. Simulations assessed MOFA2s performance with small sample sizes. Transcriptomic and microbiome data were normalized and analyzed with MOFA2, and gene set enrichment analysis (GSEA) was performed. ResultsMOFA2 demonstrated robust performance with small sample sizes in simulations and accurately recapitulated findings from published data. Analysis identified five latent factors associating the tumor transcriptome, tumor microbiome, or both with differences in tumor subtypes, ICB response, and specific irAEs. GSEA highlighted pathways related to oxidative phosphorylation, DNA replication, and immune responses. ConclusionIntegrative analysis of multi-omics data using MOFA2 provides insights into melanoma biology, uncovering distinct molecular pathways underlying clinical phenotypes. These insights contribute to our understanding of the complex biological mechanisms contributing to differences in melanoma clinical and tumor characteristics and treatment response, offering potential insight towards future development of more personalized and effective diagnostic, prognostic, and therapeutic strategies for patients. Context SummaryThis study aims to integrate multi-omics data, specifically transcriptomic and microbiome datasets, using the MOFA2 computational framework, to understand the complex interplay driving melanoma heterogeneity and response to immune checkpoint blockade (ICB) therapy. The study demonstrates that MOFA2 performs effectively even with small sample sizes, successfully capturing factors that distinguish tumor subtypes, ICB response, and immune-related adverse events (irAEs). It identifies associations between molecular features and clinical outcomes, shedding light on potential mechanisms underlying melanoma pathogenesis and treatment response. By integrating clinical and molecular data, the findings offer insights into the biological underpinnings of melanoma treatment response. Understanding these mechanisms could inform the development of more effective diagnostic, prognostic, and therapeutic strategies for melanoma patients, moving towards personalized oncology approaches.

bioinformatics↗

bioRxiv2024

Proteomic profiling of the local and systemic immune response to pediatric respiratory viral infections

Viral lower respiratory tract infection (vLRTI) is a leading cause of hospitalization and death in children worldwide. Despite this, no studies have employed proteomics to characterize host immune responses to severe pediatric vLRTI in both the lower airway and systemic circulation. To address this gap, gain insights into vLRTI pathophysiology, and test a novel diagnostic approach, we assayed 1,305 proteins in tracheal aspirate (TA) and plasma from 62 critically ill children using SomaScan. We performed differential expression (DE) and pathway analyses comparing vLRTI (n=40) to controls with non-infectious acute respiratory failure (n=22), developed a diagnostic classifier using LASSO regression, and analyzed matched TA and plasma samples. We further investigated the impact of viral load and bacterial coinfection on the proteome. The TA signature of vLRTI was characterized by 200 DE proteins (Padj<0.05) with upregulation of interferons and T cell responses and downregulation of inflammation-modulating proteins including FABP and MIP-5. A nine-protein TA classifier achieved an AUC of 0.96 (95% CI 0.90-1.00) for identifying vLRTI. In plasma, the host response to vLRTI was more muted with 56 DE proteins. Correlation between TA and plasma was limited, although ISG15 was elevated in both compartments. In bacterial coinfection, we observed increases in the TNF-stimulated protein TSG-6, as well as CRP, and interferon-related proteins. Viral load correlated positively with interferon signaling and negatively with neutrophil-activation pathways. Taken together, our study provides fresh insight into the lower airway and systemic proteome of severe pediatric vLRTI, and identifies novel protein biomarkers with diagnostic potential. IMPORTANCEWe describe the first proteomic profiling of the lower airway and blood in critically ill children with severe viral lower respiratory tract infection (vLRTI). From tracheal aspirate (TA), we defined a proteomic signature of vLRTI characterized by increased expression of interferon signaling proteins and decreased expression of proteins involved in immune modulation including FABP and MIP-5. Using machine learning, we developed a parsimonious diagnostic classifier that distinguished vLRTI from non-infectious respiratory failure with high accuracy. Comparative analysis of paired TA and plasma specimens demonstrated limited concordance, although the interferon-stimulated protein ISG15 was significantly upregulated with vLRTI in both compartments. We further identified TSG-6 and CRP as airway biomarkers of bacterial-viral coinfection, and viral load analyses demonstrated positive correlation with interferon-related protein expression and negative correlation with the expression of neutrophil activation proteins. Taken together, our study provides new insight into the lower airway and systemic proteome of severe pediatric vLRTI.

immunology↗

bioRxiv2024

Active fluctuations of cells reduce friction to enable fast and coherent collective migration

Collective cell migration is an emergent phenomenon, with long-range cell-cell communication influenced by various factors, including transmission of forces, viscoelasticity of individual cells, substrate interactions, and mechanotransduction. We investigate how alterations in cell-substrate distance fluctuations, cell-substrate adhesion, and traction forces impact the average velocity and temporal-spatial correlation of confluent monolayers formed either by wild-type MDCKII cells or zonula occludens (ZO) 1/2-depleted MDCKII cells (dKD) representing highly contractile cells. The data indicates that confluent dKD monolayers exhibit decreased average velocity compared to less contractile WT cells concomitant with increased substrate adhesion, reduced traction forces, a more compact shape, diminished cell-cell interactions, and reduced cell-substrate distance fluctuations. Depletion of basal actin and myosin further supports the notion that short-range cell-substrate interactions, particularly fluctuations driven by basal actomyosin, significantly influence the migration speed of the monolayer on a larger length scale.

biophysics↗

bioRxiv2024

miR-26 deficiency causes alterations in lens transcriptome and results in adult-onset cataract

PurposeDespite strong evidence demonstrating that normal lens development requires regulation governed by miRNAs, the functional role of specific miRNAs in mammalian lens development remains largely unexplored. MethodsA comprehensive analysis of miRNA transcripts in the newborn mouse lens, exploring both differential expression between lens epithelial cells and lens fiber cells and overall miRNA abundance was conducted by miRNA-seq. Mouse lenses lacking each of three abundantly expressed lens miRNAs: miR-184, miR-26 and miR-1 were analyzed to explore the role of these miRNAs in lens development. ResultsMice lacking all three copies of miR-26 (miR-26TKO) developed postnatal cataracts as early as 4-6 weeks of age. RNA-seq analysis of neonatal lenses from miR-26TKO mice exhibited abnormal reduced expression of a cohort of genes found to be lens-enriched and linked to cataract (e.g. Foxe3, Hsf4, Mip, Tdrd7, and numerous crystallin genes), and abnormal elevated expression of genes related to neural development (Lhx3, Neurod4, Shisa7, Elavl3), inflammation (Ccr1, Tnfrsf12a, Csf2ra), the complement pathway, and epithelial to mesenchymal transition (Tnfrsf1a, Ccl7, Stat3, Cntfr). ConclusionmiR-1, miR-184 and miR-26 are each dispensable for normal embryonic lens development. However, loss of miR-26 causes lens transcriptome changes and drives cataract formation.

developmental biology↗